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revision 1.808 by jmc, Thu May 3 22:57:27 2007 UTC revision 1.1030 by jmc, Thu Oct 16 18:38:55 2008 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
8      does not become too large (to avoid precision problems in implicit-diffusion
9      solver); update ideal_2D_oce output.
10    o pkg ggl90:
11      - in ggl90_cal.F: compute only one set of visc/diff, used to
12        step forward TKE/T/S/momentum
13      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
14        have Prandlt =1)
15    o gmredi(fm07):
16      - add lower limit on Transition layer thickness + lower limit on 1/lambda
17      - allow to set few more params from data.gmredi
18    o pkg ggl90:
19          - add missing sqrt(2) factor in computation of mixing length
20            scale in ggl90_calc.F
21            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
22    
23    checkpoint61d
24    o adjoint modifs
25      - adapt to new field rhoInSitu
26      - allow to revert from StoreDynVars2D, StoreDynVars3D
27        to individual fields
28        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
29    o store 3-D (in-situ) density in commom block (DYNVARS.h)
30     - save 1 rho computation.
31     - no longer modify T & S inland when using down_slope pkg.
32    o gad_som : allow to switch to SOM advection for T & S without corresponding
33      pickup files (using new S/R: MDS_CHECK4FILE).
34    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
35      (for useSingleCpuIO to work in multi-threaded)
36    o pkg/shelfice:
37     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
38       with SHELFICEtopoFile in data.shelfice
39     - move code for reading ice shelf topography and modifying hFacC into separate
40       subroutines of the shelfice package
41     - separate initialisation of "fixed" and "variable" variables
42     - kTopC is not (yet) replaced by kSurfC, although this is possible
43    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
44    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
45      and rename:
46      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
47      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
48    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
49    
50    checkpoint61c
51    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
52      to add mass source/sink of fluid in the interior (3-D generalisation
53      of oceanic real-fresh water flux).
54    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
55    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
56    o new pkg: down_slope
57      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
58      - presently, modify T & S inland (dwnslp_calc_rho.F).
59        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
60      - implementation for ocean in P-coords not tested.
61      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
62    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
63      (to facilitate conversion of oceanic pkg to p-coordinate).
64    o change FIND_RHO to FIND_RHO_2D :
65      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
66    o new pkg: cheapaml
67    
68    checkpoint61b
69    o exch2:
70      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
71      - no longer depend on the order sequence (N,S,E,W).
72      - 3rd exchange no longer needed (tested with 24 tiles).
73      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
74      - exch_UV_A-grid readily available (but not yet tested).
75      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
76      (both are no longer needed) in exch_uv: no effect in forward run; but
77       get truncation error differences with adjoint exch.
78    o exch2:
79     - change index-bounds storage (moved from target to local tile,
80       more intuitive this way) ; rename/remove some variables.
81     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
82    
83    checkpoint61a
84    o exch2/matlab-topology-generator:
85      fix bug in index bounds for N-S internal exchange (hard to tell if this
86      had any effect on the solution).
87    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
88      is exceeded
89    o testreport: modify syntax of awk, so that it works also with
90      awk, and not only with nawk and gawk
91    
92    checkpoint61
93    o autodiff
94      Change default for TAF usage by removing argument '-nonew_arg'
95      This changes TAF subroutine argument list (ordering of active var.)
96      Omission of this flag leads to incompatibility w.r.t. TAMC
97      To restore TAMC-compatibility, need following modifs:
98      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
99      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
100      Tested TAF version is 1.9.22
101      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
102    
103    checkpoint60
104    --->>> This is the last checkpoint for which generating the adjoint
105    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
106    --->>> by default.
107    --->>> Future checkpoints will ommit this flag by default.
108    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
109    o pkg/grdchk: Add gradient check to etan0 perturbations.
110    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
111    o pkg/autodiff: more flexibility in zeroadj.
112      model/src: modifying do_oceanic_phys.F accordingly.
113    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
114    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
115      special setup of gmredi for which the adjoint is stable
116      enough for parameter optimization.
117    o bridging the gap between eddy stress and GM.
118      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
119          along with a change in CPP option (now ALLOW_EDDYPSI).
120      -> when using GM w/ GM_AdvForm:
121          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
122          is applied either in the tracer Eq. or in momentum Eq.
123          depending on data.gmredi (intro. GM_InMomAsStress).
124      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
125      The key modifications are in model/src/taueddy_external_forcing.F
126      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
127    
128    checkpoint59r
129    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
130      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
131      fix option to read coriolis(@ cell-corner) from files with CS-grid.
132    o pkg/mnc: add some attributes to standard 1D-coordinate variables
133    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
134      mass points, when using mnc for output
135      - add runtime parameter (missing_value, missing_value_int) to override
136        default (which is the value of getcon('UNDEF'))
137    o pkg/mnc: prepare mnc for the actual use of missing values with the
138      diagnostics package: small fix in mnc_cw_readwrite.template and more
139      initialisation of never used fields
140      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
141      versions
142    o pkg/thsice/thsice_ini_vars.F added default initial values so that
143      thermodynamics sea ice solver does not blow up when some initial fields
144      are missing.
145    o move from external_forcing_surf.F to ini_forcing.F
146      the p-coord. hack consisting in using pLoad to set phi0surf ;
147      update output of tutorial_global_oce_in_p (affected @ truncation level).
148    o Freshen up a bit hs94.1x64x5, notably:
149      remove rotationPeriod and tRef=5*0. (adjoint only), and add
150      exactConserv=.TRUE.
151    o pkg/generic_advdiff:
152      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
153      applies to files where Temperature & Salinity 2nd Order moments are used.
154    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
155      this uses a dynamically allocated internal state data structure
156      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
157      and requires a fortran 90 compiler
158    
159    checkpoint59q
160    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
161       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
162    o Refresh tutorial_global_oce_biogeo, notably:
163      - change bathymetry (put back seamounts in ACC, use hFacs)
164      - change EOS (POLY3 --> JMD95Z)
165      - use Bryan-Lewis vertical diffusivity
166      - use multidimensional advection
167      - remove old virtual virtual in dic pkg, now done through ptracer pkg
168      - change a couple of parameters in dic pkg
169    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
170    o pkg/obcs: change default to OBCSfixTopo = .true.,
171      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
172      - replace "debugMode" with "debugLevel .GE. debLevB"
173    o implementation of TAF directives for gchem,cfc,dic
174    o remove "exp5" (replaced by tutorial_deep_convection).
175    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
176      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
177      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
178      --> changes results in exp4, seaice_obcs
179    o tutorial_deep_convection :
180      update the set-up and increase resolution and domain size ; start
181      from pseudo initial conditions = output at t=120mn in order to see
182      something happening when running testreport.
183    o pkg/seaice: add os7mp as an advection scheme
184                  add check for advection schemes
185                  add a flag for restoring T and S underneath sea ice
186    o pkg/my82: add netcdf-support and diagnostics
187    o thsice pkg:
188      - Now hsMax limits snow height by turning it into ice following
189        flooding scheme (and now conserving energy)
190      - Slight rewriting of the formula in thsice_calc_thick.F
191      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
192      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
193    
194    checkpoint59p
195    o gchem / dic / cfc :
196      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
197      - add new parameter files: "data.dic" & "data.cfc" ;
198      - various re-arrangement in initialisation & header file ;
199      - fix tutorial_global_oce_biogeo for multi-threaded test.
200    o pkg/dic: test for "pickup_dic" file when restarting ;
201      if no pickup-file, can restart with a re-initialised pH (same as it did
202      before) providing pickupStrictlyMatch is set to False.
203    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
204      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
205    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
206      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
207    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
208     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
209       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
210    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
211       scheme to use for vorticty-term ;
212     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
213       (with default selectVortScheme, return to original discretisation)
214     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
215    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
216    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
217      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
218      also fix diagnostics VISCAHW & VISCA4W.
219    
220    checkpoint59o
221    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
222    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
223      move a few statemens out the main loop into separate loops
224    o pkg/shelfice:
225      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
226        (kg/m^2/s), does not break tests, because in verification/isomip,
227        rhoConstFresh=rhoConst (by accident)
228      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
229      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
230        new file model/src/seawater.F, so that they are available for all pkgs.
231      - convert potential temperature into in-situ temperature. This changes the
232        isomip tests => update tests
233    o add a flag writePickupAtEnd (default=true) to be able to suppress
234      writing a pickup at the last timestep
235    o tools/mpack-1.6 :
236      - disable automake (not working) and autoconf (not needed).
237      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
238        also cleaner with much less compilation warnings.
239    o pkg/profiles:
240      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
241      (for "less than 32 characters name" compiler requirement)
242    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
243      conditions that have a different sampling frequency than S/T/U/V obcs
244    o pkg/diagnostics (stats-diags):
245      - fix global Min/Max in case 1 processor get only empty tiles
246    o genmake2: replace (4 times)
247         make genmake_tc_1.o >> genmake_warnings 2>&1
248      with
249         COMM="$CC $CFLAGS -c genmake_tc_1.c"
250         echo $COMM >> genmake_warnings
251         $COMM >> genmake_warnings 2>&1
252      to make genmake2 always see the value of CC as specified in the optfile.
253    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
254      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
255      - modify verification advect_cs test to test SOM-advection on CS-grid.
256    o pkg/ctrl:
257      - Rewrite of ctrl_map_ini_ecco.F,
258        introducing a generic routine (ctrl_map_ini_gen.F).
259      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
260    
261    checkpoint59n
262    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
263      number in dedicate array "hdiag":
264      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
265        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
266      - many small changes (integer format) for large number of diagnostics
267      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
268        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
269    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
270      usingSphericalGrid, this allows to define the rotated grid coordinates
271      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
272      geographical coordinates according to the inverse of the rotation defined
273      by the Euler angles, so that Coriolis parameter and online-interpolation by
274      exf works with the geographical coordinates on XC/YC/XG/YG.
275      Naturally, this feature does not work with all packages, so some
276      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
277      profiles), because there the coordinates are assumed to be regular
278      spherical grid coordinates.
279    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
280      - introduce isopycnal diffusion coefficient control.
281    o tools/adjoint_options:
282      - additional control vector components.
283    o pkg/mnc: have mnc create marginally meaning full coordinate variables
284      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
285    o pkg/mypackage:
286      - add example of read/write pickup for state-var ;
287      - add entry points to the main code for state-vars diags & write-pickup.
288    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
289      transitions for useExfYearlyFields
290      - add new subroutine that determines the file to read from for
291        use*YearlyFields = .TRUE. and .FALSE.
292      - add a verification experiment to global_with_exf that tests
293        useExfYearlyFields with USE_EXF_INTERPOLATION defined
294    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
295      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
296      subroutines (which could be generated from a template, because they are
297      almost identical), for now they are included in obcs_prescribe_read.F for
298      simplicity
299    o pkg/exf:
300      - add a little more diagnostic to exf_interp_read (in analogy to
301        mds_read_field, can be turned off with debugLevel < debugLevA=1)
302      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
303        ugly but fast by unrolling short inner loops, inserting a unroll=8
304        directive in routine lagran, and splitting a loop and making do while the
305        outermost loop (the latter requires the intoduction of index arrays)
306    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
307    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
308      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
309    o verification/seaice_obcs: updated for restart test and latest options
310    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
311      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
312      for now this is only available for the C-grid code and also within
313      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
314    
315    checkpoint59m
316    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
317      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
318    o gad_som : fix flux output (& diagnostics) to have same units as other  
319      advection scheme fluxes (was previously multiplied by deltaT).  
320    o added verification/seaice_obcs both to test seaice open boundaries
321      and to provide an example matlab scrpt for generating them
322    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
323    o pkg/salt_plume: clean up salt_plume_frac.F to
324      remove redundancy in PlumeMethod 1 and 4
325    o pkg/kpp: added saltplume diagnostics
326    o pkg/obcs and pkg/seaice:
327      - do not set uice and vice to zero when OB*icefile are unspecified
328      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
329      - moved seaice tracer obcs after call to seaice_growth
330    o pkg/salt_plume: added various options for salt plume depth
331      criterion and for vertical distribution of the salt
332    
333    checkpoint59l
334    o pkg/ptracers: new version of ptracers pickup:
335      read meta file and write only fields which are needed to restart.
336      ( same logic as main pickup file ; also using pickupStrictlyMatch )
337    o pkg/seaice:
338      - add timescale for melting due to warm mixed layer as a means of
339        setting SEAICE_availHeatFrac more conveniently
340      - add a CPP-flag/runtime parameter check for flooding algorithm
341      - reformulated availHeat in seaice_growth.F to be independent of AREA
342    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
343      unit changes
344    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
345    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
346      SX vector computer.
347    o pkg/seaice:
348      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
349        seaice forcing fields can now be read only through pkg/exf
350      - removed some unused halos
351    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
352    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
353      or U/VICE from U/VWIND before computing U/VSTRESS
354    
355    checkpoint59k
356    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
357      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
358    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
359      all experiments pass when compile with un-initialised var. checking option.
360    o added pkg/salt_plume
361    o script to test restart (for now, in MITgcm_contrib/jmc_script)
362    o pkg/seaice: new read/write pickup version.
363      read meta file and write only fields which are needed to restart.
364      ( same logic as main pickup file ; also using pickupStrictlyMatch )
365    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
366    o lab_sea.hb87: modify the domain & update output.hb87.txt :
367      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
368      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
369      process. Fixed here by closing the domain at the Northern boundary.
370    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
371    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
372      a set of consecutive levels in/from a 3-D array.
373    o pkg/ptracers:
374      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
375      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
376    
377    checkpoint59j
378    o in pkgs: dic, obcs, offline, rbcs:
379      standard way to compute coeff. for time interpolation between 2 time reccords
380      which retains full precision (& make results less dependent on compiler).
381      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
382    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
383      packages instead of reading ice cover and wind speed separately
384    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
385     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
386      to allow to compile customized code before the update)
387    o cleaning-up:
388      - fix CPP instruction syntax in pkg/obcs
389      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
390        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
391      - fix some threads issue in IO parts.
392    o pkg/dic:
393      - add tons of "_d 0" (--> much better testreports !)
394       and then update outputs of tutorial_global_oce_biogeo
395    o pkg/mom_fluxform:
396      add a special version of momentum advection intended to conserve momentum
397      next to a bathymetry step or a coastline edge. (default = off = #undef)
398    o new read/write pickup version:
399      - for now, only implemented for main (mdsio) pickup file.
400      - write out only what is needed to restart; merge pickup_nh , pickup_ph
401        and main pickup together.
402      - read meta file; read only what is needed to restart; stop if a field
403        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
404        if it make sense (even if the restart is not perfect).
405      - if no meta file, assume that pickup to read corresponds exactly to
406        a pickup that would currently be written.
407      - read pickup written in the old format (until checkpoint59i) if it
408        recognizes an old meta file (no field-list).
409      - add a meta file in exp. which starts from a pickup: 2 cases:
410        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
411         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
412        b) a meta file describing the content of the associated pickup file
413         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
414    o pkg/mdsio & pkg/rw:
415      - new routine to read a meta file ; new set of routine to read
416        Multiple-fields file (with meta file).
417    o added open boundary conditions capability for seaice
418        HSNOW, HSALT, UICE, and VICE
419    
420    checkpoint59i
421    o adjoint:
422      * fix multiDimAdvection adjoint
423        (partial recomputation problem by TAF for fVerT(:,:,kDown)
424        and comlev1 size definition (maxpass vs. max. number of tracers)
425      * verification/global_ocean.90x45x15 adjoint now tests
426        NLFS and multiDimAdvection using DST3 (=30)
427      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
428    o pkg/kpp: add "_d 0" to real constant (if missing);
429      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
430      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
431    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
432      for internal parameters related to restart process (formerly from PARAMS.h)
433      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
434    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
435      as argument. (only atm2d & obcs write_pickup have not yet been updated)
436    o pkg/monitor:
437      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
438      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
439      - account for deep Atmosphere factor and density factor (anelastic)
440    o added open boundary conditions capability for seaice HEFF and AREA
441    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
442      thermodynamics
443      - requires a little reorganization, which affects the testreport results
444        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
445        so that now the conservative form is tested
446      - add a few comments
447    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
448    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
449    o add new diagnostics to seaice: advective, diffusive fluxes (only for
450      multidim-advection, for scheme 2 they are not filled) and transports,
451      thermodynamic growth rates
452    o change units of EmPmR (inside the code, + within coupling interface)
453      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
454      Affects results @ truncation level (cg2d match) and update output of
455       experiments: lab_sea(6), global_ocean.90x40x15(10),
456      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
457      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
458      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
459      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
460    
461    checkpoint59h
462    o pkg/exf:
463      - improve vectorization by moving if-statement out of loops in
464        exf_mapfields, exf_radiation
465      - exf_bulkformulae.F: introduce 2D fields and vectorize code
466    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
467    o testreport:
468      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
469        monitor & update offline_exf_seaice exp. output.
470      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
471    o pkg/seaice:
472      - bug fix in the evp solver: boundary conditions were affected be
473        masking of zMax/zMin (changes results)
474      - minor bug fix in boundary conditions in seaice_calc_strainrates
475        (changes results for no_slip)
476      - seaice_lsr.F: make interpolation of eta dependent on boundaries
477      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
478      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
479        stress formulation and no-slip boundary conditions
480    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
481      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
482    o pkg/seaice: a first HSALT time stepping equation has been checked in
483    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
484      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
485      without requiring DO-IF statements
486    o pkg/thsice:
487      use continuous power-law function for partition of energy between lateral
488      melting/freezing and thinning/thickening ; old code using step function
489      still available with #undef THSICE_FRACEN_POWERLAW
490      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
491    o testreport: change AD testing : check against results/output_adm.txt
492      using same scripts as for forward test.
493    
494    checkpoint59g
495    o adjoint testing: in preparation for changing testreport:
496      - output format: cost and grad written on separated lines
497      - ad output results in directory "results" (instead of "results_ad")
498    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
499    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
500    o pkg/ecco: allow user defined cost function contributions
501    o testreport:
502      Allow to choose (per experiment) the list of tested output variables
503       and the main variable (used to issue a pass/FAIL ) ;
504      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
505      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
506      Also modify printing of summary:
507       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
508       b) echo the list of tested variables in the individual summary.txt of
509          each experiment.
510    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
511      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
512      (but still depend on the tile decompostion of the domain).
513    o pkg/seaice: change a discretization detail to make the B-grid code
514      "more symmetric". This change is likely to remove all "ridges/leads" that
515      where quasi-aligned with the grid in B-grid solutions. It may also be
516      the solution to the stress coupling issues with the B-grid.
517    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
518      remove .cvsignore from input dir. (since testreport no longer run here).
519    o pkg/thsice:
520     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
521     - fix reshaping of sea-ice just after advection:
522       melt all the ice only if ice-volume is too small.
523     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
524       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
525     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
526    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
527      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
528    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
529      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
530      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
531      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
532      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
533      -> update output.txt
534    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
535     this affects truncation error: -> update output.txt of exp:
536      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
537      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
538    
539    checkpoint59f
540    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
541    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
542      a bounded range (in forward mode)
543    o pkg/ecco, ctrl, autodiff and mom_common:
544     internal parameter controls, completements of implementations
545    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
546    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
547      (not seem any difference in testing results).
548    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
549       at face corners.
550    o pkg/generic_advdiff:
551     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
552      loop range indices for computing vertical advection tendency
553      and do the calculation in the interior only (no overlap) ;
554      for now, only implemented for SOM advection (to save CPU time).
555     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
556    o exch2 adjoint
557      First set of changes:
558      - add exch2 hand-written adjoint templates
559      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
560        This will require cleanup in pkg/autodiff/*.F
561        (changed routines currently kept separate in verif. code/)
562      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
563        that used to hide exch2 or cubed-sphere specific code
564        (commented via 'cph-exch2')
565    o pkg/seaice
566      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
567    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
568       output of global_ocean.cs32x15.thsice .
569    
570    checkpoint59e
571    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
572      for B-grid vector (not yet tested) and C-grid vector (<- only used
573      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
574    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
575      (#ifdef ALLOW_SALT_PLUME)
576    o gather_2d/scatter_2d: removed halo regions
577    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
578      scheme and the corresponding test case (under front_relax dir). For now,
579      only available with Skew-flux form and not yet tested in realistic set-up.
580      adjoint: store directives updated, but gradient checks deteriorated,
581      so maybe GM/Redi adjoint is now broken.
582    o seaice adjoint
583      * add AREA, HEFF, HSNOW as control variable
584        (should not change lab_sea results)
585      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
586    o pkg/seaice:
587      * added computation of saltFlux in seaice_growth;
588        For time being, sea ice salinity is assumed constant
589        contribution of snow flooding to freshening of sea ice is neglected.
590        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
591        defaults to 0.0 in order to maintain backward compatibility.
592        Typical values for SEAICE_salinity are 4 to 10 g/kg.
593      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
594      * added SEAICE_availHeatFrac, which specifies fraction of surface level
595        heat content used to melt or grow ice
596      * commented out cap of HICE: it helps keep ice thinner
597      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
598      * applied OBCS T/S mask to HEFFM sea ice mask
599    
600    checkpoint59d
601    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
602     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
603     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
604    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
605     and change default value of parameter "GM_Small_Number";
606     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
607       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
608       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
609    o pkg/ecco: cost function when applying pkg/smooth to controls
610    o pkg/ctrl: add forcingPrecond run time parameter
611    o pkg/seaice:
612     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
613     - fix bug in metric terms of u-equation in LSR solver (implicit part),
614       changes verification/lab_sea
615     - rearrange implicit part of u-equation in LSR solver to make it easier to
616       read, understand, and debug. This causes changes at the truncation level.
617     - fix (serious) bug in the boundary conditions (sign error in the implicit
618       part) of the LSR solver. Changes all LSR results.
619     - fixed problem with HSNOW initialization to avoid thick snow when AREA
620       is initilized with small values - does not change lab_sea results.
621     - added HsnowFile initialization capability
622    o pkg/smooth: addition to model/src and pkg/ctrl so allow
623     initialization of pkg/smooth and application to control vector
624    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
625    o dependencies: pkg/profiles requires pkg/cal
626    o pkg/profiles:
627     - added option ALLOW_PROFILES_GENERICGRID
628         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
629         that interpolation information (grid points and coefficients) is provided
630         within the netcdf input files.
631         -> sample matlab scripts can be found in MITgcm_contrib/gael
632         that allow you to prepare netcdf input files.
633     - also modified: cleaner include statements, cleaner error print statements,
634       cleaner stops when error, and more tests of the netcdf input files consistency.
635    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
636    o pkg/seaice:
637     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
638       requires a new routine: seaice_diagnostics_fill.F
639     - make sure that seaice does not move if not forced (pressure replacement
640       method, Hibler and Ip, 1995), changes results
641     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
642     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
643       It is turned off by default (=-1.), because it changes the results.
644     - make it possible to read AREA from a file, too.
645    
646    checkpoint59c
647    o add S/R and diagnostics for oceanic mixed-layer depth
648    o move GMRedi call after all vertical mixing schemes (including KPP)
649    o pkg/thsice:
650     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
651      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
652    o pkg/obcs:
653     - bug fix for balance code
654    o pkg/seaice:
655      - allow values of SEAICE_elasticParm > 1
656      - add new parameter SEAICE_evpTauRelax as an alternative
657        to SEAICE_elasticParm
658      - make lsr boundary conditions free slip (by default), changes result
659      - add code for no slip boundary conditions for lsr
660      - set minimum of zeta to zero (and not 4e8) (changes results)
661      - add a cap on AREA after advecting AREA if seaice_growth is not called
662    o change calculation of Visbeck K:
663      - no longer depend on tapering scheme; instead, compute slope (limited
664        by GM_maxSlope). this is equivalent to what was comuted before with
665        clipping or linear tappering.
666      - fix vertical averaging (wrong by 1/2 level)
667      - leave the old version (but will not be maintained) within
668        #ifdef OLD_VISBECK_CALC / #endif
669      - update output of exp. ideal_2D_oce
670    o change error catch in calc_r_star to improve vectorization
671    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
672      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
673    o adjoint:
674      Re-organized adjoint checkpointing according to Matt Mazloff
675      (but with modifs/completions/cleanups)
676      Storing is now bundled into large arrays to optimized I/O
677      (and second step in cleanup of the_main_loop)
678    
679    checkpoint59b
680    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
681      - export/import (between ocean & coupler) fields needed for ocean DIC.
682    o pkg/seaice:
683      - get rid of three more exchanges seaice_calc_viscosities (required
684        different loop boundaries in seaice_lsr and seaice_ocean_stress)
685      - bug fix in seaice_ocean_stress (update of lab_sea required)
686      - reduce loop boundaries to necessary minimum also in seaice_evp
687      - go back to the old way of computing deltaC/Z as the adjoint likes that
688        better
689    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
690      passive tracer to an Age Tracer) + update output.txt
691    o pkg/exf:
692      - implement A-grid / C-grid selection for wind-stress input files.
693      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
694      for now, in exf_bulk_largeyeager04.F only :
695      - change implementation for case where windspeed + 2. components wind-stress
696        are read-in. AND use rhoConstFresh to convert evap.
697    o pkg/seaice:
698      - use correct EXCH_UV for wind-forcing (on A-grid).
699      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
700        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
701    o pkg/exf:
702      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
703      EXF_INTERPOLATION:
704      - merge global_with_exf/code version of exf_interp_read.F
705        to the main code ;
706      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
707        reading the file ; Important: This options needs to be defined to recover
708        previous code.
709        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
710      - no longer loose real*8 precision along the way when using exf_iprec=64.
711    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
712      - change discretisation of evp-solver in order to avoid another exchange
713        (changes lab_sea) and clean up a little
714      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
715        help the adjoint (this also changes the results slightly)
716      - add a few "_d 0" where they had been missing in seaice_evp.F
717      - cleaning up: remove unused seaice_calc_rhs.F
718    o pkg/exf: some cleaning-up:
719      - change various "constants" into runtime parameters
720      - cleaned-up Large&Yeager04 routine which should eventually
721        replace exf_bulkformulae.F (changed names of S/R and CPP)
722        and merged various ALLOW_ATM_WIND options
723     only used with thsice pkg (in thsice_get_exf.F):
724      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
725        which are used when useStabilityFct_overIce=TRUE (= the default)
726      - change default values of ice & snow emissivity and scale downward LW
727        by ice & snow emissivity.
728    o pkg/thsice:
729     fix few little problems, in thsice_calc_thickn.F:
730      - growth vertically (and not laterally) if iceFrac == iceMaskMax
731      - melt only laterally if hIce < hThinIce (as the comments say)
732      and in thsice_extend.F:
733      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
734      - start to form ice as soon as the minimum ice-volume is reachable.
735     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
736      and cpl_aim+ocn
737  o pkg/kpp  o pkg/kpp
  - remove wrong (within bi,bj loops) EXCH calls.  
  - little cleaning (add argument myThid in last position, cvs header ...)  
738   - move computation of surface related input fields to KPP into a new   - move computation of surface related input fields to KPP into a new
739     subroutine kpp_forcing_surf.F     subroutine kpp_forcing_surf.F
740     - remove wrong (within bi,bj loops) EXCH calls.
741     - little cleaning (add argument myThid in last position, cvs header ...)
742     - for now, fix conservation problem by exchanging KPPviscAz (may not
743       be the best fix)
744  o pkg/seaice  o pkg/seaice
745   - check for inconsistent evp parameter/cpp-flag combination   - check for inconsistent evp parameter/cpp-flag combination
746   - remove leftover errIO flat for obsolete name list error handling   - remove leftover errIO flat for obsolete name list error handling
747    o OpenAD
748     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
749    
750  checkpoint59a  checkpoint59a
751  o pkg/seaice: some parameter clarifications and a little bit of clean up  o pkg/seaice: some parameter clarifications and a little bit of clean up
# Line 31  o in FFIELDS.h: Line 765  o in FFIELDS.h:
765       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
766  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
767  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
768      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
769        are no longer updating the vertical diffusivity array
770        (passed as argument) but are (re-) setting those arrays.
771  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
772    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
773      cgrid-lsr and evp solver      cgrid-lsr and evp solver
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